Turner 2004

Exterior Loop

Example

Free Energy Change

Prediction of Stacking

The predicted stacking configuration is the one with lowest free energy change. There are two possible configurations.

Configuration 1:

Helix 1 with 5' dangling U, Helix 2 with 3' dangling C, and Helix 3 with a GG mismatch

∆G°37 = ∆G°37(AU with 5' dangling U) + ∆G°37(CG with 3' dangling C) + ∆G°37(CG with GG mismatch)

∆G°37 = –0.2 kcal/mol 0.8 kcal/mol – 1.6 kcal/mol

∆G°37 = –2.6 kcal/mol

Configuration 2:

Helix 1 in a flush coaxial stack with Helix 2 and Helix 3 with a GG mismatch

∆G°37 = ∆G°37(coaxial stack of AU followed by GC) + ∆G°37(CG with GG mismatch)

∆G°37 = –2.08 kcal/mol 1.6 kcal/mol

∆G°37 = –3.7 kcal/mol

Therefore, configuration 2, -3.7 kcal/mol, is the predicted free energy change.

Enthalpy Change

Prediction of Stacking

The stacking configuration is fixed by the prediction of folding free energy change and is configuration 2 above.

∆H°= ∆H°(coaxial stack of AU followed by GC) + ∆H°(CG with GG mismatch)

∆H°= –10.5 kcal/mol 9.2 kcal/mol

∆H° = –19.7 kcal/mol